I had the same experience in my 00 Passat 4 motion.....the manual states that the VW OEM changer mixes several songs on one CD before switching...I found it to play almost the whole CD every time, in addition, it repeated a song every so often.
Check the manual and see if it sheds any light, but it doesn't sound unusual to me.
Of course, the MP3 install (using spockcat's instructions) is quite simple, and the sound is as good as the changer.....
Smitty